An industrial tribunal ordered him to pay pounds 6,089 to Catherine Wray, who the Glasgow Ballieston MP had accused at a hearing earlier this month of waging a "vendetta" against him.
The three-man tribunal ruled that he had unfairly dismissed her as his secretary last May.
In its written findings, the tribunal said the essence of Mr Wray's case was that her employment had ended with the dissolution of Parliament.
But the tribunal determined: "The tribunal was unable to accept that the applicant's employment was brought to an end by performance of a specified task or project.
"The work which she was employed to do was secretarial duties. There was no evidence that the applicant's employment was other than continuous from June 1987 until her employment was terminated almost ten years later on April 30 1997.
"At that time the need for secretarial services still remained."
Mrs Wray had no immediate comment on her victory, a spokesman for her said yesterday.
The ruling followed a tribunal hearing earlier this month in Glasgow at which Mr Wray, 63, a former boxer, made an emotional and bitter attack on his estranged wife. After the hearing, he revealed his that girlfriend, Laura Walker, was pregnant and they hoped to marry soon.
His marriage to Catherine took place in 1985. The tribunal's written findings stated she worked part-time as his secretary from June 1987 from the matrimonial home. Her duties included contact with constituents, taking phone calls, and forwarding mail.
But by 1994 the pair were living in separate rooms in the matrimonial home, said the tribunal. They separated in the following year and Mr Wray moved out while she remained in their house in Glasgow.